Variant report

Variant	rs16844254
Chromosome Location	chr4:3389270-3389271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3294234..3297919-chr4:3387466..3390148,3	MCF-7	breast:
2	chr4:3385272..3387718-chr4:3389014..3391654,3	MCF-7	breast:
3	chr4:3388642..3391528-chr4:3405332..3407484,2	MCF-7	breast:
4	chr4:3388406..3390149-chr4:3442407..3445401,2	MCF-7	breast:
5	chr4:3388256..3390546-chr4:3393263..3395293,2	MCF-7	breast:
6	chr4:3386285..3389665-chr4:3485168..3487566,3	MCF-7	breast:
7	chr4:3356602..3361196-chr4:3388835..3391854,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10007038	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10035011	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049879	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13435851	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1406673	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844251	0.88[LWK][hapmap]
rs16844260	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844272	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844277	0.92[ASW][hapmap]
rs28410709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28420539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28457232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28489501	0.85[AFR][1000 genomes]
rs28505211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28535968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28636983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58249502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61527677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446736	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446737	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446738	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446739	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812029	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6825183	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6829410	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847900	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792011	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792031	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7656119	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9291160	0.88[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3375400-3389600	Weak transcription	NHLF	lung
2	chr4:3378400-3390400	Weak transcription	Ovary	ovary
3	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
4	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
5	chr4:3386200-3390000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:3386400-3390800	Enhancers	Fetal Lung	lung
8	chr4:3386400-3391200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:3386600-3390800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:3386800-3389600	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:3386800-3393600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr4:3386800-3393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:3387200-3389600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:3387400-3389600	Enhancers	HUVEC	blood vessel
18	chr4:3387400-3389800	Weak transcription	Fetal Intestine Large	intestine
19	chr4:3387600-3389600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:3387600-3390600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr4:3387600-3390600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:3387600-3392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:3387800-3389600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:3387800-3389800	Weak transcription	Primary T cells from cord blood	blood
25	chr4:3387800-3389800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:3387800-3391000	Active TSS	Esophagus	oesophagus
27	chr4:3388000-3390200	Active TSS	HMEC	breast
28	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:3388200-3389600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:3388200-3389800	Enhancers	Brain Substantia Nigra	brain
31	chr4:3388400-3389600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:3388400-3390000	Enhancers	Fetal Kidney	kidney
33	chr4:3388400-3391200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:3388400-3392000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr4:3388400-3393600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:3388600-3389400	Enhancers	Lung	lung
37	chr4:3388600-3389400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:3388600-3389400	Enhancers	Spleen	Spleen
39	chr4:3388600-3389600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr4:3388600-3389800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr4:3388600-3390000	Enhancers	Left Ventricle	heart
42	chr4:3388600-3392000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:3388600-3392400	Enhancers	Fetal Muscle Trunk	muscle
44	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:3388800-3389400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr4:3388800-3389400	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr4:3388800-3389400	Enhancers	Brain Hippocampus Middle	brain
48	chr4:3388800-3389400	Enhancers	Stomach Mucosa	stomach
49	chr4:3388800-3389600	Enhancers	Primary B cells from cord blood	blood
50	chr4:3388800-3389600	Enhancers	Primary hematopoietic stem cells	blood

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